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Coexpression cluster:C311: Difference between revisions

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{{Coexpression_clusters
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|full_id=C311_rectal_heart_choriocarcinoma_placenta_chorionic_lung_ductal
|id=C311
}}

Latest revision as of 11:19, 17 September 2013


Full id: C311_rectal_heart_choriocarcinoma_placenta_chorionic_lung_ductal



Phase1 CAGE Peaks

Hg19::chr11:118826999..118827014,+p1@UPK2
Hg19::chr11:86502063..86502074,+p26@PRSS23
Hg19::chr11:86502085..86502118,+p13@PRSS23
Hg19::chr11:89901127..89901133,+p@chr11:89901127..89901133
+
Hg19::chr12:31632584..31632589,-p20@DENND5B
Hg19::chr12:31632597..31632607,-p13@DENND5B
Hg19::chr12:57410306..57410318,-p1@TAC3
Hg19::chr15:54134723..54134734,+p@chr15:54134723..54134734
+
Hg19::chr1:172421915..172421926,+p4@C1orf105
Hg19::chr1:172421997..172422007,+p3@C1orf105
Hg19::chr1:172422026..172422039,+p2@C1orf105
Hg19::chr1:172422041..172422055,+p1@C1orf105
Hg19::chr1:43533230..43533270,+p@chr1:43533230..43533270
+
Hg19::chr1:90420182..90420201,+p@chr1:90420182..90420201
+
Hg19::chr20:3999149..3999160,-p@chr20:3999149..3999160
-
Hg19::chr2:191384421..191384433,-p@chr2:191384421..191384433
-
Hg19::chr2:191384465..191384471,-p@chr2:191384465..191384471
-
Hg19::chr2:197124712..197124735,+p2@ENST00000430904
Hg19::chr2:209864821..209864831,-p@chr2:209864821..209864831
-
Hg19::chr4:10048437..10048443,+p@chr4:10048437..10048443
+
Hg19::chr4:175309496..175309506,+p@chr4:175309496..175309506
+
Hg19::chr6:125540918..125540931,+p6@TPD52L1
Hg19::chr6:31683061..31683070,+p5@LY6G6D
Hg19::chr6:31683080..31683091,+p2@LY6G6D
Hg19::chr6:31683117..31683130,+p1@LY6G6D
Hg19::chr6:31683157..31683167,+p3@LY6G6D
Hg19::chr7:12007288..12007295,-p@chr7:12007288..12007295
-
Hg19::chr7:12125449..12125453,-p@chr7:12125449..12125453
-
Hg19::chr7:12134329..12134354,-p@chr7:12134329..12134354
-
Hg19::chr7:12134356..12134370,-p@chr7:12134356..12134370
-
Hg19::chr7:12134371..12134377,-p@chr7:12134371..12134377
-
Hg19::chr7:12134400..12134410,-p@chr7:12134400..12134410
-
Hg19::chr7:12250342..12250347,+p@chr7:12250342..12250347
+
Hg19::chr7:16873035..16873059,-p6@AGR2
Hg19::chr7:27282288..27282293,-p2@ENST00000519050
Hg19::chr7:27282416..27282426,+p1@EVX1
Hg19::chr8:120164231..120164239,+p@chr8:120164231..120164239
+
Hg19::chr9:20732373..20732384,+p@chr9:20732373..20732384
+
Hg19::chr9:286553..286563,+p@chr9:286553..286563
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
rectum3.10e-504
lower digestive tract1.48e-405
large intestine2.25e-1911
intestine1.85e-1217
hindgut6.95e-1219
gastrointestinal system4.34e-0925
Disease
Ontology termp-valuen
gastrointestinal system cancer1.43e-1514


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.14.20904e-06
MA0004.10.0566508
MA0006.10.014912
MA0007.10.0501273
MA0009.10.88381
MA0014.13.54077e-09
MA0017.10.453168
MA0019.10.777862
MA0024.10.254518
MA0025.10.439186
MA0027.11.8466
MA0028.10.204475
MA0029.10.739626
MA0030.10.720769
MA0031.10.61691
MA0038.10.32871
MA0040.10.272523
MA0041.10.492494
MA0042.10.428611
MA0043.10.332327
MA0046.10.323723
MA0048.10.020072
MA0050.10.753892
MA0051.12.87446
MA0052.10.755709
MA0055.10.556996
MA0056.10
MA0057.10.250203
MA0058.10.0279236
MA0059.10.0276133
MA0060.10.245358
MA0061.10.312888
MA0063.10
MA0066.10.100184
MA0067.10.597968
MA0068.10.0517652
MA0069.10.320777
MA0070.10.312273
MA0071.10.991148
MA0072.10.308875
MA0073.11.06826e-06
MA0074.10.0975962
MA0076.10.561822
MA0077.10.303076
MA0078.10.45889
MA0081.10.115503
MA0083.10.337888
MA0084.10.768496
MA0087.10.82764
MA0088.10.0232086
MA0089.10
MA0090.12.33572
MA0091.10.0575983
MA0092.10.170933
MA0093.10.0154139
MA0095.10
MA0098.10
MA0100.10.705366
MA0101.10.190552
MA0103.10.564235
MA0105.10.066982
MA0106.10.12076
MA0107.10.0343864
MA0108.22.53851
MA0109.10
MA0111.15.00762
MA0113.10.406016
MA0114.10.366131
MA0115.10.530757
MA0116.10.035858
MA0117.10.36143
MA0119.10.473302
MA0122.10.382044
MA0124.10.494979
MA0125.10.42437
MA0130.10
MA0131.10.161082
MA0132.10
MA0133.10
MA0135.10.355725
MA0136.10.103403
MA0139.10.00123664
MA0140.10.582341
MA0141.11.18534
MA0142.11.07776
MA0143.11.31209
MA0144.10.0268501
MA0145.10.114108
MA0146.10.000132192
MA0147.10.0070378
MA0148.10.505562
MA0149.10.0768601
MA0062.20.0345451
MA0035.22.01204
MA0039.20.000499644
MA0138.20.151138
MA0002.20.364553
MA0137.20.0845704
MA0104.20.0169579
MA0047.20.367013
MA0112.20.0545862
MA0065.20.0348416
MA0150.10.585392
MA0151.10
MA0152.10.284971
MA0153.10.41053
MA0154.10.0634095
MA0155.10.00922847
MA0156.10.217366
MA0157.11.59915
MA0158.10
MA0159.10.0376607
MA0160.10.537314
MA0161.10
MA0162.14.57437e-08
MA0163.10.00265022
MA0164.10.423404
MA0080.20.186056
MA0018.20.385322
MA0099.20.597378
MA0079.25.88536e-07
MA0102.20.803155
MA0258.10.163134
MA0259.10.00790712
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
TAL1#688653.829309830441050.009376508648130890.0353860369553423



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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